OCA Atlas for 1TZI

1TZI

Immune System

date

Jul 10, 2004

title

Crystal Structure Of The Fab Yads2 Complexed With H-Vegf

authors

F.A.Fellouse, C.Wiesmann, S.S.Sidhu

compound

source

Molecule: Fab Yads2 Light Chain
Chain: A
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 16c9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: F0771-B6

Molecule: Fab Yads2 Heavy Chain
Chain: B
Engineered: Yes

Molecule: Vascular Endothelial Growth Factor A
Chain: V
Synonym: Vegf-A, Vascular Permeability Factor, Vpf, H-Vegf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vegf, Vegfa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: C 2 2 21

R_factor

0.218

R_Free

0.254

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
96.504	149.588	117.421	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.80 Å

related structures

by homologous chain: 1AI1, 1BZQ, 1FL6, 1KAT, 1QTY

Gene
Ontology

Chain	Function	Process	Component
V

Primary reference

Synthetic antibodies from a four-amino-acid code: A dominant role for tyrosine in antigen recognition., Fellouse FA, Wiesmann C, Sidhu SS, Proc Natl Acad Sci U S A 2004 Aug 24;101(34):12467-72. Epub 2004 Aug 11. PMID:15306681

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]

Biological Unit Coordinates (1tzi.pdb1.gz) 161 Kb

CSU: Contacts of Structural Units for 1TZI

Likely Quarternary Molecular Structure file(s) for 1TZI

Structure Factors (161 Kb)

Retrieve 1TZI in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1TZI from S2C, [Save to disk]

Re-refined 1tzi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1TZI in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1TZI

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1TZI, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1tzia1, region A:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1tzia2, region A:108-211 [Jmol] [rasmolscript] [script source]
- Domain d1tzib1, region B:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1tzib2, region B:114-213 [Jmol] [rasmolscript] [script source]
- Domain d1tziv_, region V [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1tzi_V] [1tzi] [1tzi_A] [1tzi_B]

SWISS-PROT database: [P15692]

Domain organization of [VEGFA_HUMAN] by SWISSPFAM

Domains found in 1TZI: [IG_like] [IGv] [PDGF ] by SMART

Other resources with information on 1TZI

Community annotation for 1TZI at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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